Here is the full list of all 99 Time Clickers achievements. It takes around 200 hours to unlock all of the achievements on Windows.
Destroy 50.0M Cubes
Time Warp 25 Times
Beat Wave 750
Get a Team Member to Spec Ops 2 (LVL 2,000)
Collect 1.00t Gold (Total)
Collect 1.00r Gold (Total)
Beat Wave 550
Defeat Wave 500 Boss
Collect 1.00p Gold (Total)
Collect 1.00n Gold (Total)
Collect 1.00l Gold (Total)
Beat Wave 350
Collect 999i Gold (Total)
Shoot Click Pistol 250K Times
Upgrade a Team Member 2.00K Times
Destroy 1.50M Yellow Cubes
Destroy 5.00M Cubes
Time Warp 10 Times
Defeat Wave 250 Boss
Get a Team Member to Spec Ops 1 (LVL 1,000)
Collect 999g Gold (Total)
Destroy 1.00M White Cubes
Get Team DPS to 10.0f
Beat Wave 200
Destroy 150K Yellow Cubes
Destroy 500K Red Cubes
Get Team DPS to 10.0e
Collect 999e Gold (Total)
Shoot Click Pistol 100K Times
Earn 50.0e Gold
Get 10.0K Critical Strikes
Get Team DPS to 10.0d
Time Warp 5 Times
Shoot Click Pistol 50.0K Times
Upgrade a Team Member 500 Times
Time Warp 3 Times
Collect 1.00d Gold (Total)
Get Team DPS to 10.0c
Destroy 5,000 Rainbow Cubes
Get 1.00K Critical Strikes
Get Team DPS to 10.0b
Destroy 100K White Cubes
Destroy 500K Cubes
Upgrade a Team Member 125 Times
Time Warp 1 Time
Beat Wave 100
Defeat Wave 100 Boss
Earn 250a Gold
Get Team DPS to 10.0a
Get Team DPS to 10.0Q
Destroy 50.0K Red Cubes
Collect 1.00Q Gold (Total)
Get 100 Critical Strikes
Get Team DPS to 10.0T
Earn 5.00T Gold
Destroy 50.0K Cubes
Upgrade a Team Member 50 Times
Beat Wave 50
Get Team DPS to 10.0B
Collect 1.00B Gold (Total)
Shoot Click Pistol 10.0K Times
Upgrade a Team Member 25 Times
Get Team DPS to 10.0M
Beat Wave 25
Collect 1.00M Gold (Total)
Earn 500K Gold
Upgrade a Team Member 5 Times
Destroy 5.00K Cubes
Shoot Click Pistol 1.00K Times
Shoot Click Pistol 500 Times
Beat Wave 10
Shoot Click Pistol 100 Times
Beat Wave 950
Beat Wave 1,150
Beat Wave 1,350
Beat Wave 1,550
Beat Wave 1,850
Beat Wave 2,150
Beat Wave 2,450
Beat Wave 2,750
Beat Wave 3,000
Defeat Wave 1,000 Boss
Defeat Wave 2,000 Boss
Defeat Wave 3,000 Boss
Time Warp 50 Times
Time Warp 100 Times
Time Warp 250 Times
Destroy 1,000 Rainbow Balls
Upgrade a Team Member 5.00K Times
Upgrade a Team Member 12.5K Times
Upgrade a Team Member 25.0K Times
Destroy 75.0M Cubes
Get a Team Member to Spec Ops 3 (LVL 3,000)
Get a Team Member to Spec Ops 4 (LVL 4,000)
Get a Team Member to Spec Ops 5 (LVL 5,000)
Collect 5.00M Time Cubes
Collect 3.00M Weapon Cubes
Beat Wave 3,500
Defeat Wave 4,000 Boss